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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Use when building ANY watchOS app — app structure, independent apps, Watch Connectivity, Smart Stack widgets, complications, controls, RelevanceKit, background tasks, ClockKit migration.

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Use when asking about Axiom skills or axbuild build/test capture, xclog console, xcsym .ips/MetricKit/.crash symbolication, xcui simulator UI/accessibility, or xcprof xctrace/CPU profiles.

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Use when the user mentions TextKit review, text layout issues, Writing Tools integration, or UITextView/NSTextView code review.

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Use when building ANY 2D or 3D game with SpriteKit, SceneKit, or RealityKit, or adding touch controls or game controller support. Covers scene graphs, ECS, physics, actions, game loops, rendering, TouchController, GCController.

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Use when making visual or interaction design decisions for an Apple app — HIG patterns, Liquid Glass, SF Symbols, typography, app entry-point and auth-flow structure.

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Build SwiftUI layouts using stacks, grids, lists, scroll views, forms, and controls. Covers VStack/HStack/ZStack, LazyVGrid/LazyHGrid, List with sections and swipe actions, ScrollView with ScrollPosition and scroll-driven reveal surfaces, Form with validation, Toggle/Picker/Slider, .searchable, and overlay patterns. Use when building data-driven layouts, collection views, paged detail reveals, settings screens, search interfaces, or transient overlay UI.

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Apply modern Swift language patterns and idioms for non-concurrency, non-SwiftUI code. Covers if/switch expressions (Swift 5.9+), typed throws (Swift 6+), result builders, property wrappers, opaque and existential types (some vs any), guard patterns, Never type, Regex builders (Swift 5.7+), basic Codable shaping (CodingKeys, custom decoding, nested containers), modern collection APIs (count(where:), contains(where:), replacing()), basic FormatStyle usage, and string interpolation patterns. Use when writing core Swift code involving generics, protocols, enums, closures, or modern language features; route deep Codable to swift-codable, detailed formatting/localization to swift-formatstyle, and API naming to swift-api-design-guidelines.

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Builds and reviews SwiftUI views with modern MV architecture, state, composition, isolated previews, and migration guidance. Covers @Observable ownership, @State/@Bindable/@Environment wiring, view decomposition, ViewModifiers, environment values, .task loading, iOS 26+ handoffs, Writing Tools, clipboard availability, and performance. Use when structuring SwiftUI state, managing @Observable, composing views, previewing meaningful UI states, or correcting SwiftUI patterns.

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Embeds and controls web content in SwiftUI with WebKit for SwiftUI, including WebView, WebPage, navigation policies, JavaScript execution, observable page state, link interception, local HTML or data loading, and custom URL schemes. Use when building iOS 26+ article/detail views, help centers, in-app documentation, or other embedded web experiences backed by HTML, CSS, and JavaScript.

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Implement, review, or improve SwiftUI Liquid Glass effects for iOS 26+. Covers glassEffect modifier, GlassEffectContainer, glass button styles, glass toolbar/tab bar, static status badges vs interactive controls, morphing transitions, tinting, interactive glass, ToolbarSpacer, scrollEdgeEffectStyle, backgroundExtensionEffect, and availability gating. Use when asked about Liquid Glass, glass buttons, glassEffect, GlassEffectTransition, glassEffectID, glassEffectUnion, scroll edge effects, or adopting iOS 26 design.

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Use when capturing or analyzing ETTrace profiles for a focused iOS launch or runtime flow, including exact-build dSYM UUID matching, Simulator or device capture, processed per-thread flamegraph JSON, sampled inclusive/exclusive time, unresolved symbols, and comparable verification. Use debugging-instruments or swiftui-performance for generic profiling instead.

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Add drawings, shapes, and a consistent markup experience using PaperKit. Use when integrating PaperMarkupViewController for markup editing, adding shape recognition, working with PaperMarkup data models, embedding markup tools in document editors, or building annotation features that need the system-standard markup toolbar. New in iOS 26.

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Query grid electricity forecasts and submit load events using EnergyKit to help users optimize home electricity usage. Use when building smart home apps, EV charger controls, HVAC scheduling, or energy management dashboards that guide users to use power during cleaner or cheaper grid periods.

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Create media playback experiences using AVKit. Use when adding video players with AVPlayerViewController, enabling Picture-in-Picture, routing media with AirPlay, using SwiftUI VideoPlayer views, configuring transport controls, displaying subtitles and closed captions, or integrating AVFoundation playback with system UI.

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Use when capturing or analyzing an iOS .memgraph, especially when the task mentions a memory leak, heap growth, persistent memory increase, ownership path, or matched-capture comparison with Apple CLI tools. Covers unambiguous Simulator capture, leaks/heap/vmmap/malloc_history evidence, raw artifact preservation, and same-flow verification. Use debugging-instruments for interactive Xcode Memory Graph, Instruments, generic retain-cycle inspection, or LLDB work.

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Integrate Apple Music playback, catalog search, and Now Playing metadata using MusicKit and MediaPlayer. Use when adding music search, Apple Music subscription flows, queue management, playback controls, remote command handling, or Now Playing info to iOS apps.

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Search runtime and scene management: verify queries, inspect scenes, debug app readiness, and diagnose recall or scene-config issues.

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Volcengine official documentation lookup helper. Supports both document search and full-content fetch across Volcengine products, developer tools, support content, best practices, pricing, deployment, troubleshooting, API, SDK, and policy pages.

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Writes turn-level tests for a LiveKit agent in the user's normal test suite: pytest (Python) or Vitest (Node.js). Use when the user asks to "write tests for my agent", "add a test for this tool", "test the handoff", "pin this bug", "why does my agent test fail", or after building or changing agent behavior that needs regression coverage. Covers the SDK's test session harness, assertions on messages, tool calls and handoffs, LLM judging of a reply against an intent, mocking tools, multi-turn tests, and judging whole conversations with the built-in judges. For interactive poking use debugging-livekit-agents. For grading whole conversations at scale use running-livekit-simulations.

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Use when tasks involve reading, creating, or reviewing PDF files where rendering and layout matter; prefer visual checks by rendering pages (Poppler) and use Python tools such as `reportlab`, `pdfplumber`, and `pypdf` for generation and extraction.

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